[Bioc-devel] BiocManager not installing latest release version of DepecheR

[Nicolas Delhomme]

I have faced the same issue as described in this post and I agree with Aaron, that it would be nice if the doc on the website where extended to specify the version as in "BiocManager::install(version='3.10’)"

Best,

Nico

> On 15 Nov 2019, at 00:32, Aaron Lun <infinite.monkeys.with.keyboards using gmail.com> wrote:
> 
> I would assume that "BiocManager::install()" won't update an existing
> set of BioC packages unless explicitly prompted. If that's the case,
> shouldn't the instructions at http://bioconductor.org/install/ specify
> "BiocManager::install(version='3.10')"?
> 
> On Wed, Nov 13, 2019 at 1:04 PM Shepherd, Lori
> <Lori.Shepherd using roswellpark.org> wrote:
>> 
>> BiocManager should recognize versions automatically for the version of R.  I believe we had a message that would be displayed in this case where there was a more recent version available
>> Something along the lines of:
>> Bioconductor version '3.9' is out-of-date; the current release version '3.10'
>>  is available with R version '3.6'; see https://bioconductor.org/install
>> 
>> It is broken in this latest version of BiocManager but will be correct shortly.
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> 
>> ________________________________
>> From: Jakob Theorell <jakob.theorell using ndcn.ox.ac.uk>
>> Sent: Wednesday, November 13, 2019 3:59 PM
>> To: Aaron Lun <infinite.monkeys.with.keyboards using gmail.com>; Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
>> Subject: Re: [Bioc-devel] BiocManager not installing latest release version of DepecheR
>> 
>> Yes, this sounds like a very good solution. Thank you all for your input, and I hope this silly mistake of mine might have some positive consequence.
>> Best
>> Jakob
>> ________________________________
>> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Aaron Lun <infinite.monkeys.with.keyboards using gmail.com>
>> Sent: 13 November 2019 18:56
>> To: Shepherd, Lori <Lori.Shepherd using roswellpark.org>
>> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
>> Subject: Re: [Bioc-devel] BiocManager not installing latest release version of DepecheR
>> 
>> Perhaps the installation instructions on each package's landing page
>> should explicitly specify 'version=3.10' (or whatever happens to be
>> the latest release) in the install() call. This avoids ambiguities
>> with using the latest version when the current and previous releases
>> are on the same version of R.
>> 
>> -A
>> 
>> On Wed, Nov 13, 2019 at 8:25 AM Shepherd, Lori
>> <Lori.Shepherd using roswellpark.org> wrote:
>>> 
>>> It looks like you are still installing release 3.9 versions of packages.  The latest version is release 3.10.
>>> 
>>> If you do
>>> BiocManager::version()
>>> Does it show "3.9"  or "3.10"?
>>> 
>>> I'm betting "3.9"
>>> 
>>> You can do
>>> 
>>> BiocManager::install(version="3.10")
>>> BiocManager::install()
>>> 
>>> 
>>> To update all packages to 3.10 versions
>>> 
>>> 
>>> Cheers,
>>> 
>>> 
>>> Lori Shepherd
>>> 
>>> Bioconductor Core Team
>>> 
>>> Roswell Park Comprehensive Cancer Center
>>> 
>>> Department of Biostatistics & Bioinformatics
>>> 
>>> Elm & Carlton Streets
>>> 
>>> Buffalo, New York 14263
>>> 
>>> ________________________________
>>> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Jakob Theorell <jakob.theorell using ndcn.ox.ac.uk>
>>> Sent: Wednesday, November 13, 2019 11:06 AM
>>> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
>>> Subject: [Bioc-devel] BiocManager not installing latest release version of DepecheR
>>> 
>>> Dear all,
>>> This is probably a mistake on my side, but I just now tried to install the last release version of DepecheR (for which I am the maintainer), and although the source package on BioConductor is 1.2, this is the text I get from BiocManager when installing:
>>> 
>>> Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
>>> Installing package(s) 'DepecheR'
>>> trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/DepecheR_1.0.3.tgz'
>>> 
>>> This is clearly the old version, that does not contain all the updates that the source package contains. Have I missed something I should have done to prevent this and what can I in that case do now?
>>> Best regards
>>> Jakob Theorell, MD/PhD
>>> Autoimmune Neurology Group
>>> Nuffield Department of Clinical Neurosciences
>>> University of Oxford
>>> 
>>> 
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